[R] pseudoreplication

[James Henson]

Greetings R Community
The ASReml-R package will analyze data from experiments with
pseudoreplications.

Dealing with Pseudo-Replication in Linear Mixed Models
https://www.vsni.co.uk/case-studies/dealing-with-pseudo-replication-in-linear-mixed-models

Will the ‘lme4’ package return an equivalent analysis of data from
experiments with pseudoreplications?
Thank you for your assistance.

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Error in loadNamespace

[James Henson]

Thanks David!, that fixed the problem.
Best regards,
James

On Thu, Dec 7, 2017 at 1:19 PM, David Winsemius <dwinsem...@comcast.net>
wrote:

>
> > On Dec 7, 2017, at 10:47 AM, James Henson <jfhens...@gmail.com> wrote:
> >
> > Hello R Community,
> >
> > I inadvertently updated packages via R Studio when a package was open.
> Now
> > when R Studio is opened the message below appears in the console panel.
> >
> > Error in loadNamespace(name) : there is no package called ‘yaml’
> >
> > Error in loadNamespace(name) : there is no package called ‘yaml’
> >
> > When running R code, so far the only function that has not worked is
> > datatable () in the ‘DT’ package.  Removing the ‘DT’ package and
> > reinstalling it had no effect.  A possible fix is to update R from an
> older
> > version, which was not running when I made the mistake.  Is this a good
> > idea?
>
> There is a package on CRAN named "yaml". Have your tried installing it?
> >
> > Thanks for your help.
> >
> > James F. Henson
> >
> >   [[alternative HTML version deleted]]
>
> Rhelp is a plain text mailing list.
>
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
> David Winsemius
> Alameda, CA, USA
>
> 'Any technology distinguishable from magic is insufficiently advanced.'
>  -Gehm's Corollary to Clarke's Third Law
>
>
>
>
>
>

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] Error in loadNamespace

[James Henson]

Hello R Community,

I inadvertently updated packages via R Studio when a package was open.  Now
when R Studio is opened the message below appears in the console panel.

Error in loadNamespace(name) : there is no package called ‘yaml’

Error in loadNamespace(name) : there is no package called ‘yaml’

When running R code, so far the only function that has not worked is
datatable () in the ‘DT’ package.  Removing the ‘DT’ package and
reinstalling it had no effect.  A possible fix is to update R from an older
version, which was not running when I made the mistake.  Is this a good
idea?

Thanks for your help.

James F. Henson

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] Bayes Factor

[James Henson]

Hello R Community;

Just posted a question about Bayes Factor.  But, just answered my own question.
What is needed is to convert a 'dplyr' data frame into a standard data frame.
competition2 <- data.frame(competition), where 'competition' is a
'dplyr' data frame with the following class structure.
[1] "tbl_df"  "tbl"  "data.frame".

Best regards,
James

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] Bayes Factor

[James Henson]

Hello R Community,
Subject: Bayes Factor
A Bayesian ANOVA of the form:
competitionBayesOut <- anovaBF(biomass ~ clipping, data = competition)
Returns the following Error message:
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘compare’ for
signature ‘"BFlinearModel", "missing", "tbl_df"’

My guess the problem is in the ‘class’, which is:
[1] “tbl_df”  “tbl”  “data.frame”
The data was imported via the ‘readr’ package through R Studio, and
then saved as a RData file.
My code is below, and the data is attached as a text file.

Thanks for your assistance.
Best regards,
James

# Plots for Interpreting One-Way ANOVA

library(digest)

library(DT)

datatable(competition)

# Characterize the data.

class(competition)

str(competition)

competition$clipping <- as.factor(competition$clipping)

competition$biomass <- as.numeric(competition$biomass)

str(competition)

#

tapply(competition$biomass, competition$clipping, mean)

tapply(competition$biomass, competition$clipping, sd)





# Bayesian Procedure for ANOVA



# Calculate Bayes Factors

library(BayesFactor)

competitionBayesOut <- anovaBF(biomass ~ clipping, data = competition)

# Run mcmc iterations

mcmcOut2 <- posterior(competitionBayesOut, iterations = 1)

# boxplot of the posteriors for the groups

boxplot(as.matrix(mcmcOut2[,2:6]))

# Show the HDIs

summary(mcmcOut2)

# Calculate the Bayes Factor

competitionBayesOut



# Pairwise "post hoc" tests

library(rjags)

library(BEST)



# competitionare 'r5' vs. 'control'

plot(BESTmcmc(competition[competition$clpping=="r5",2],
competition[competition$clipping=="control",2]))

#

plot(BESTmcmc(competition[competition$clpping=="r10",2],
competition[competition$clipping=="control",2]))

# competitionare 'n10' vs. 'control'

plot(BESTmcmc(competition[competition$clipping=="n10",2],
competition[competition$clipping=="control",2]))

# competitionare 'n50' vs. 'control'

plot(BESTmcmc(competition[competition$clipping=="n50",2],
competition[competition$clipping=="control",2]))
clippingbiomass
n25 551
n25 457
n25 450
n25 731
n25 499
n25 632
n50 595
n50 580
n50 508
n50 583
n50 633
n50 517
r5  639
r5  615
r5  511
r5  573
r5  648
r5  677
control 417
control 449
control 517
control 438
control 415
control 555
r10 563
r10 631
r10 522
r10 613
r10 656
r10 679
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Marg.fct function

[James Henson]

Greetings Peter and Jeff,

Thanks for this information.  Will try these type of analyses in SAS.
Sure they are doable in R, but developing a procedure is difficult.
Alan Agresti gives a cookbook SAS method in An Introduction to
Categorical Analysis.

Thanks,
James

On Sun, Feb 5, 2017 at 3:47 PM, Jeff Newmiller <jdnew...@dcn.davis.ca.us> wrote:
> It is not part of "R". You can dig through all of the packages that the 
> author mentions,  or send an email to the author.
> --
> Sent from my phone. Please excuse my brevity.
>
> On February 5, 2017 11:44:40 AM PST, James Henson <jfhens...@gmail.com> wrote:
>>Greetings R Community,
>>
>>An attempt to reproduce the results from code in the source below
>>fails.  R cannot find the function ‘Marg.fct’. An Internet search for
>>the ‘Marg.fct’ function was not fruitful.  I appreciate your help.
>>Best regards, James F. Henson.
>>
>>R (and S-PLUS) Manual to Accompany Agresti’s Categorical Data Analysis
>>(2002) 2nd edition Laura A. Thompson, 2009©
>>
>>http://www.stat.ufl.edu/~aa/cda/Thompson_manual.pdf  page 181
>>
>>The code is:
>>
>># Code from Manual to Accompany Agresti’s Categorical Data Analysis
>>(2002) 2nd edition Laura A. Thompson, 2009
>>
>>y <- c(144, 33, 84, 126, 2, 4, 14, 29, 0, 2, 6, 25, 0, 0, 1, 5)
>>
>>ZF <- Z <- matrix(1,16,1)
>>
>>#
>>
>>M1 <- Marg.fct(1,rep(4,2)) # used to get m1+, etc
>>
>>Error: could not find function "Marg.fct"
>>
>>
>>
>>M2 <- Marg.fct(2,rep(4,2)) # used to get m+1, etc
>>
>>#
>>
>>C.matrix <- matrix(c(
>>
>>  1, 0, 0, 0, -1, 0, 0, 0, # y1+ = y+1
>>
>>  0, 1, 0, 0, 0, -1, 0, 0, # y2+ = y+2
>>
>>  0, 0, 1, 0, 0, 0, -1, 0), # y3+ = y+3
>>
>>  3,8,byrow=T)
>>
>>h.fct <- function(m) { # constraint function
>>
>> marg <- rbind(M1%*%m, M2%*%m) # y1+, y2+, y3+, y4+, y+1, y+2, y+3, y+4
>>
>>  C.matrix%*%marg # y1+ = y+1, y2+ = y+2, etc
>>
>>}
>>
>>#
>>
>>a <- mph.fit(y=y,Z=Z,ZF=ZF,h.fct=h.fct)
>>
>>mph.summary(a)
>>
>>__
>>R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>https://stat.ethz.ch/mailman/listinfo/r-help
>>PLEASE do read the posting guide
>>http://www.R-project.org/posting-guide.html
>>and provide commented, minimal, self-contained, reproducible code.

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] Marg.fct function

[James Henson]

Greetings R Community,

An attempt to reproduce the results from code in the source below
fails.  R cannot find the function ‘Marg.fct’. An Internet search for
the ‘Marg.fct’ function was not fruitful.  I appreciate your help.
Best regards, James F. Henson.

R (and S-PLUS) Manual to Accompany Agresti’s Categorical Data Analysis
(2002) 2nd edition Laura A. Thompson, 2009©

http://www.stat.ufl.edu/~aa/cda/Thompson_manual.pdf  page 181

The code is:

# Code from Manual to Accompany Agresti’s Categorical Data Analysis
(2002) 2nd edition Laura A. Thompson, 2009

y <- c(144, 33, 84, 126, 2, 4, 14, 29, 0, 2, 6, 25, 0, 0, 1, 5)

ZF <- Z <- matrix(1,16,1)

#

M1 <- Marg.fct(1,rep(4,2)) # used to get m1+, etc

Error: could not find function "Marg.fct"



M2 <- Marg.fct(2,rep(4,2)) # used to get m+1, etc

#

C.matrix <- matrix(c(

  1, 0, 0, 0, -1, 0, 0, 0, # y1+ = y+1

  0, 1, 0, 0, 0, -1, 0, 0, # y2+ = y+2

  0, 0, 1, 0, 0, 0, -1, 0), # y3+ = y+3

  3,8,byrow=T)

h.fct <- function(m) { # constraint function

  marg <- rbind(M1%*%m, M2%*%m) # y1+, y2+, y3+, y4+, y+1, y+2, y+3, y+4

  C.matrix%*%marg # y1+ = y+1, y2+ = y+2, etc

}

#

a <- mph.fit(y=y,Z=Z,ZF=ZF,h.fct=h.fct)

mph.summary(a)

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] confidence intervals for orthogonal contrasts

[James Henson]

Richard,

Thanks, Have not previously used the HH package, but looks as if it
contains many useful tools.  Will check out your book also.

Best regards,
James

On Thu, Dec 1, 2016 at 10:18 PM, Richard M. Heiberger <r...@temple.edu> wrote:
> James,
>
> Please look at the maiz example, the last example in ?MMC
> help("MMC", package="HH")
> where I show how to construct and calculate a set of orthogonal contrasts
> for a factor in an analysis of variance setting.  mmc and mmcplot use glht
> in the multcomp package for the underlying calculations.
>
> If yo don't have HH, you can get it with
> install.packages("HH")
>
> See the references in ?MMC to my book and paper.  The second edition
> of the book is now available.
>
> Rich
>
> On Thu, Dec 1, 2016 at 4:17 PM, James Henson <jfhens...@gmail.com> wrote:
>> Hi R users,
>> Is there a way to calculate a confidence interval for each contrast in
>> a set of orthogonal contrasts?  The ‘multcomp’ package will calculate
>> a CIs at the 95% family-wise confidence level.  But, these confidence
>> intervals are extremely wide.
>> Thanks for your help.
>> Best regards,
>> James
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] confidence intervals for orthogonal contrasts

[James Henson]

Hi R users,
Is there a way to calculate a confidence interval for each contrast in
a set of orthogonal contrasts?  The ‘multcomp’ package will calculate
a CIs at the 95% family-wise confidence level.  But, these confidence
intervals are extremely wide.
Thanks for your help.
Best regards,
James

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] yuen function of the WRS2 package

[James Henson]

Thanks,
The 'droplevels' statement works.
Best regards,
James Henson

On Tue, Aug 30, 2016 at 5:34 PM, William Dunlap <wdun...@tibco.com> wrote:
> yuen does not work when there unused levels in the factors given to it.
>
>>  yuen(GoalsGame ~ League, tr=0.2, data = SpainGer)
> Call:
> yuen(formula = GoalsGame ~ League, data = SpainGer, tr = 0.2)
>
> Test statistic: NaN (df = NA), p-value = NA
>
> Trimmed mean difference:  NaN
> 95 percent confidence interval:
> NaN NaN
>
>>  yuen(GoalsGame ~ League, tr=0.2, data = droplevels(SpainGer))
> Call:
> yuen(formula = GoalsGame ~ League, data = droplevels(SpainGer),
> tr = 0.2)
>
> Test statistic: 0.8394 (df = 16.17), p-value = 0.4135
>
> Trimmed mean difference:  -0.11494
> 95 percent confidence interval:
> -0.405 0.1751
>
> Complain to WSR2's maintainer.
>> maintainer("WRS2")
> [1] "Patrick Mair <m...@fas.harvard.edu>"
>
>
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
> On Tue, Aug 30, 2016 at 2:07 PM, James Henson <jfhens...@gmail.com> wrote:
>>
>> Greetings R community,
>> Here is a small but perplexing problem with the ‘yuen’ function in the
>> ‘WRS2’ package.
>> I begin with the ‘eurosoccer’ data frame from the ‘WRS2’ package.
>> Then make a subset that contains only two Leagues Spain and Germany
>> (subset data frame is ‘SpainGer’).   The ‘yuen’ function cannot read
>> the data in subset data frame ‘SpainGer’.  My code is below.
>> Thanks you for your help.
>> James F. Henson
>>
>>
>> # Examples from 'Robust Statistical Methods on R Using the WRS2 Package’
>> # Robust t-test, and ANOVA (pages5-13)
>> library(WRS2)
>> data("eurosoccer")
>> class(eurosoccer)
>> print(eurosoccer)
>> library("digest")
>> library("DT")
>> datatable(eurosoccer)
>> str(eurosoccer)
>> # make a subset with only Spain and Germany
>> SpainGer <- subset (eurosoccer, subset = League =="Spain" | League ==
>> "Germany")
>> print(SpainGer)
>> class(SpainGer)
>> str(SpainGer)
>> # The 'yuen' function can not read the data in the subset data.frame
>> "SpainGer"
>> yuen(GoalsGame ~ League, tr=0.2, data = SpainGer)
>> # the 'yuen' function works on the orginioal data.frame
>> yuen(GoalsGame ~ League, tr=0.2, data = eurosoccer)
>> # the 'aov' function reads the data in the subset data.frame "SpainGer"
>> Goals.fit <- aov(GoalsGame ~ League, data = SpainGer)
>> summary(Goals.fit)
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
>

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] yuen function of the WRS2 package

[James Henson]

Greetings R community,
Here is a small but perplexing problem with the ‘yuen’ function in the
‘WRS2’ package.
I begin with the ‘eurosoccer’ data frame from the ‘WRS2’ package.
Then make a subset that contains only two Leagues Spain and Germany
(subset data frame is ‘SpainGer’).   The ‘yuen’ function cannot read
the data in subset data frame ‘SpainGer’.  My code is below.
Thanks you for your help.
James F. Henson


# Examples from 'Robust Statistical Methods on R Using the WRS2 Package’
# Robust t-test, and ANOVA (pages5-13)
library(WRS2)
data("eurosoccer")
class(eurosoccer)
print(eurosoccer)
library("digest")
library("DT")
datatable(eurosoccer)
str(eurosoccer)
# make a subset with only Spain and Germany
SpainGer <- subset (eurosoccer, subset = League =="Spain" | League == "Germany")
print(SpainGer)
class(SpainGer)
str(SpainGer)
# The 'yuen' function can not read the data in the subset data.frame "SpainGer"
yuen(GoalsGame ~ League, tr=0.2, data = SpainGer)
# the 'yuen' function works on the orginioal data.frame
yuen(GoalsGame ~ League, tr=0.2, data = eurosoccer)
# the 'aov' function reads the data in the subset data.frame "SpainGer"
Goals.fit <- aov(GoalsGame ~ League, data = SpainGer)
summary(Goals.fit)

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Whether statistical background is must to learn R language

[James Henson]

Greetings Prasad,

Here are some tutorials on statistics using R.Statistics and Actuarial
Science – Carl James Schwarz

http://people.stat.sfu.ca/~cschwarz/CourseNotes/



Statistics and Actuarial Science – Carl James Schwarz - Programs

http://people.stat.sfu.ca/~cschwarz/Stat-650/Notes/MyPrograms/



Design Analysis and Interpretation of Experiments

http://www.unh.edu/halelab/BIOL933/

Great YouTube channel of R tutorials by Mike Marin,

https://www.youtube.com/user/marinstatlectures

Best regards,
James


On Tue, May 31, 2016 at 8:04 AM, PIKAL Petr  wrote:
> Hi
>
> Well, it seems to me like cooking.
>
> You does not have to be educated cook to be able prepare some food in your 
> kitchen, but knowledge of some recipes can lead to tasty results
>
> Regards
> Petr
>
>> -Original Message-
>> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Prasad
>> Kale
>> Sent: Tuesday, May 31, 2016 9:23 AM
>> To: R-help@r-project.org
>> Subject: [R] Whether statistical background is must to learn R language
>>
>> Hi,
>>
>> I am very new to R and just started learning R. But i am not from statistical
>> background so can i learn R or to learn R statistical background is must.
>>
>> Please guide.
>>
>> Thanks in Advance
>> Prasad
>>
>>   [[alternative HTML version deleted]]
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-
>> guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> 
> Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou 
> určeny pouze jeho adresátům.
> Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě neprodleně 
> jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie vymažte ze 
> svého systému.
> Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email 
> jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat.
> Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi či 
> zpožděním přenosu e-mailu.
>
> V případě, že je tento e-mail součástí obchodního jednání:
> - vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření smlouvy, 
> a to z jakéhokoliv důvodu i bez uvedení důvodu.
> - a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout; 
> Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany 
> příjemce s dodatkem či odchylkou.
> - trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve výslovným 
> dosažením shody na všech jejích náležitostech.
> - odesílatel tohoto emailu informuje, že není oprávněn uzavírat za společnost 
> žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn nebo písemně 
> pověřen a takové pověření nebo plná moc byly adresátovi tohoto emailu 
> případně osobě, kterou adresát zastupuje, předloženy nebo jejich existence je 
> adresátovi či osobě jím zastoupené známá.
>
> This e-mail and any documents attached to it may be confidential and are 
> intended only for its intended recipients.
> If you received this e-mail by mistake, please immediately inform its sender. 
> Delete the contents of this e-mail with all attachments and its copies from 
> your system.
> If you are not the intended recipient of this e-mail, you are not authorized 
> to use, disseminate, copy or disclose this e-mail in any manner.
> The sender of this e-mail shall not be liable for any possible damage caused 
> by modifications of the e-mail or by delay with transfer of the email.
>
> In case that this e-mail forms part of business dealings:
> - the sender reserves the right to end negotiations about entering into a 
> contract in any time, for any reason, and without stating any reasoning.
> - if the e-mail contains an offer, the recipient is entitled to immediately 
> accept such offer; The sender of this e-mail (offer) excludes any acceptance 
> of the offer on the part of the recipient containing any amendment or 
> variation.
> - the sender insists on that the respective contract is concluded only upon 
> an express mutual agreement on all its aspects.
> - the sender of this e-mail informs that he/she is not authorized to enter 
> into any contracts on behalf of the company except for cases in which he/she 
> is expressly authorized to do so in writing, and such authorization or power 
> of attorney is submitted to the recipient or the person represented by the 
> recipient, or the existence of such authorization is known to the recipient 
> of the person represented by the recipient.
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, 

Re: [R] mixed models

[James Henson]

Greetings David,
I am new to R and neglected to check vigorously for missing values.
Apologize for posting without checking and finding the one NA.

I appreciate your help.
Thanks.
James F. Henson

On Fri, May 27, 2016 at 1:49 PM, David Winsemius <dwinsem...@comcast.net> wrote:
>
>> On May 27, 2016, at 10:07 AM, James Henson <jfhens...@gmail.com> wrote:
>>
>> Greetings Jeff,
>> You are correct that the unequal number of levels is not the problem.
>> I revised the data frame so that the number of levels was equal and
>> the same error message occurred.  The code is below, and the
>> Eboni2.txt file is attached. This problem baffles me.  I appreciate
>> any help.
>> Best regards,
>> James
>> Eboni2 <- read.csv("Eboni2.csv", header = TRUE)
>>
>> library("nlme")
>>
>> str(Eboni2)
>>
>> head(Eboni2)
>>
>> model1 <- lme(preDawn ~ Irrigation, random=~season_order|treeNo, data=Eboni2)
>
> I downloaded the attached file to your first posting that was called a "csv" 
> file but it was tab-separated (as could be clearly seen with the str output, 
> so would only load properly with read.delim rather than read.csv. Running 
> then with the lme call, it produced this message
>
>> model1 <- lme(preDawn ~ Irrigation, random=~season_order|treeNo, data=Eboni2)
> Error in na.fail.default(list(season_order = c(5L, 5L, 5L, 5L, 5L, 5L,  :
>   missing values in object
>
> And looking at the str result made it clear that there were many NA's in the 
> file.
>
>> head(Eboni2)
>   number Location   Season season_order Month  treeID treeNo preDawn midday
> 1  1  UCC November5   Nov UCCLO 1 60 1.41.3
> 2  2  UCC November5   Nov UCCLO 2 72 1.21.3
> 3  3  UCC November5   Nov UCCLO 3 78 1.11.2
> 4  4  UCC November5   Nov UCCLO 4 79 1.12.1
> 5  5  UCC November5   Nov UCCLO 5 80 1.41.3
> 6  6  UCC November5   Nov UCCLO 6 81 0.61.8
>   Irrigation PnetGsE  WUE d15N   d13C Nper  Cper include2
> 1  N9 0.2907004 3.766207 2.389672   NA NA   NANA   no
> 2  N   11 0.3262582 3.120574 3.524993   NA NA   NANA   no
> 3  N8 0.2870957 1.693821 4.723050 3.00 -27.44 2.12 52.12  yes
> 4  N   10 0.2475180 1.839343 5.436724 3.61 -29.50 1.42 51.97  yes
> 5  N   13 0.3009228 3.082278 4.217660   NA NA   NANA   no
> 6  N   17 0.3487337 2.534550 6.707304 2.79 -30.50 1.49 49.94  yes
>
> And even more importantly, there was one NA in your outcome variable:
>> sum( is.na(Eboni2$Irrigation))
> [1] 0
>> sum( is.na(Eboni2$preDawn))
> [1] 1
>
> So after restricting to complete.cases, I then formed the hypothesis that you 
> reversed the order of the variables in the formula for the random parameter:
>
>> table(Eboni2$season_order)
>
>  1  2  3  4  5
> 83 83 83 83 83
>> length( Eboni2$treeNo)
> [1] 415
>
> So it seemed unreasonable to have a "grouping" on variable with only one item 
> per group.
>
>> model1 <- lme(preDawn ~ Irrigation, random=~treeNo|season_order, 
>> data=Eboni2[ complete.cases( Eboni2[ , 
>> c('preDawn','Irrigation','season_order','treeNo')]), ] )
>> model1
> Linear mixed-effects model fit by REML
>   Data: Eboni2[complete.cases(Eboni2[, c("preDawn", "Irrigation", 
> "season_order",  "treeNo")]), ]
>   Log-restricted-likelihood: -183.4708
>   Fixed: preDawn ~ Irrigation
> (Intercept) IrrigationY
>  1.04520145 -0.06037706
>
> Random effects:
>  Formula: ~treeNo | season_order
>  Structure: General positive-definite, Log-Cholesky parametrization
> StdDev  Corr
> (Intercept) 0.140239324 (Intr)
> treeNo  0.003766019 -0.725
> Residual0.365678898
>
> Number of Observations: 414
> Number of Groups: 5
>
> (Warning, I'm not a frequent user of this package or any of the mixed effects 
> packages.)
>
>
>
> Just to correct some misinformation that appeared earlier: You can attach 
> "csv" or "tsv" files as long as you name them with an .txt extension so the 
> mail clients and servers consider them to be MIME-text.
>
> --
> David.
>
>
>> On Wed, May 25, 2016 at 6:23 PM, Jeff Newmiller
>> <jdnew...@dcn.davis.ca.us> wrote:
>>> Please keep the mailing list in the loop by using reply-all.
>>>
>>> I don't think there is a requirement that the number of levels is 

Re: [R] mixed models

[James Henson]

Greetings Jeff,
You are correct that the unequal number of levels is not the problem.
I revised the data frame so that the number of levels was equal and
the same error message occurred.  The code is below, and the
Eboni2.txt file is attached. This problem baffles me.  I appreciate
any help.
Best regards,
James
 Eboni2 <- read.csv("Eboni2.csv", header = TRUE)

library("nlme")

str(Eboni2)

head(Eboni2)

model1 <- lme(preDawn ~ Irrigation, random=~season_order|treeNo, data=Eboni2)

On Wed, May 25, 2016 at 6:23 PM, Jeff Newmiller
<jdnew...@dcn.davis.ca.us> wrote:
> Please keep the mailing list in the loop by using reply-all.
>
> I don't think there is a requirement that the number of levels is equal, but
> there may be problems if you don't have the minimum number of records
> corresponding to each combination of levels specified in your model.
>
> You can change the csv extension to txt and attach for the mailing list. Or,
> better yet, you can use the dput function to embed the data directly in your
> sample code.
>
> Also, please learn to post plain text email to avoid corruption of R code by
> the HTML formatting.
> --
> Sent from my phone. Please excuse my brevity.
>
> On May 25, 2016 2:26:54 PM PDT, James Henson <jfhens...@gmail.com> wrote:
>>
>> Good afternoon Jeff,
>> The sample sizes for levels of the factor "Irrigation" are not equal. If
>> 'nlme' requires equal sample sizes this may be the problem. The same data
>> frame runs in 'lme4' without a problem.
>>
>> Best regards,
>> James
>>
>>
>> On Wed, May 25, 2016 at 3:41 PM, James Henson <jfhens...@gmail.com> wrote:
>>>
>>> Good afternoon Jeff,
>>>
>>> When working with this data frame, I just open the .csv file in R Studio.
>>> But, we should not send .csv file to R_help.  What should I send?
>>>
>>> Best regards,
>>> James
>>>
>>> On Wed, May 25, 2016 at 2:52 PM, Jeff Newmiller
>>> <jdnew...@dcn.davis.ca.us> wrote:
>>>>
>>>> You forgot to show the commands to us that you used to read the data in
>>>> with (your example is not "reproducible"). This step can make all the
>>>> difference in the world as to whether your analysis commands will work or
>>>> not.
>>>> --
>>>> Sent from my phone. Please excuse my brevity.
>>>>
>>>> On May 25, 2016 11:59:06 AM PDT, James Henson <jfhens...@gmail.com>
>>>> wrote:
>>>>>
>>>>> Greetings R community,
>>>>>
>>>>> My aim is to analyze a mixed-effects model with temporal
>>>>> pseudo-replication
>>>>> (repeated measures on the same experimental unit) using ‘nlme’.
>>>>> However,
>>>>> my code returns the error message “Error in na.fail.default’, even
>>>>> though
>>>>> the data frame does not contain missing values. My code is below, and
>>>>> the
>>>>> data file is attached as ‘Eboni2.txt.
>>>>>
>>>>> library("nlme")
>>>>>
>>>>> str(Eboni2)
>>>>>
>>>>> head(Eboni2)
>>>>>
>>>>> model1 <- lme(preDawn ~ Irrigation, random=~season_order|treeNo,
>>>>> data=Eboni2)
>>>>>
>>>>> I am genuinely confused.  Hope someone can help.
>>>>>
>>>>> Best regards,
>>>>>
>>>>> James F. Henson
>>>>>
>>>>> 
>>>>>
>>>>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>> PLEASE do read the posting guide
>>>>> http://www.R-project.org/posting-guide.html
>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>>
>>
>

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] mixed models

[James Henson]

Greetings R community,

My aim is to analyze a mixed-effects model with temporal pseudo-replication
(repeated measures on the same experimental unit) using ‘nlme’.  However,
my code returns the error message “Error in na.fail.default’, even though
the data frame does not contain missing values. My code is below, and the
data file is attached as ‘Eboni2.txt.

library("nlme")

str(Eboni2)

head(Eboni2)

model1 <- lme(preDawn ~ Irrigation, random=~season_order|treeNo,
data=Eboni2)

I am genuinely confused.  Hope someone can help.

Best regards,

James F. Henson
number  LocationSeason  season_orderMonth   treeID  treeNo  preDawn 
midday  Irrigation  PnetGs  E   WUE d15Nd13CNper
Cperinclude2
1   UCC November5   Nov UCCLO 1 60  1.4 1.3 
N   9   0.290700373 3.766207481 2.38967185  
no
2   UCC November5   Nov UCCLO 2 72  1.2 1.3 
N   11  0.326258186 3.120573618 3.524992949 
no
3   UCC November5   Nov UCCLO 3 78  1.1 1.2 
N   8   0.287095701 1.693820753 4.723049937 3   -27.44  
2.1252.12   yes
4   UCC November5   Nov UCCLO 4 79  1.1 2.1 
N   10  0.247517983 1.83934285  5.436724317 3.61-29.5   
1.4251.97   yes
5   UCC November5   Nov UCCLO 5 80  1.4 1.3 
N   13  0.300922817 3.082277827 4.217660032 
no
6   UCC November5   Nov UCCLO 6 81  0.6 1.8 
N   17  0.348733689 2.534550345 6.70730413  2.79-30.5   
1.4949.94   yes
7   UCC November5   Nov UCCLO 7 82  0.9 1.2 
N   12  0.272690759 1.809851748 6.630377328 2.43-29.4   
1.5553.12   yes
8   UCC November5   Nov UCCLO 8 83  1.4 1.1 
N   11  0.269862804 1.919849835 5.729614785 2.85-28.37  
1.7853.52   yes
9   UCC November5   Nov UCCLO 9 84  0.8 1   
N   16  0.32333 2.394825767 6.68107059  2.43-30.1   
1.5452.88   yes
10  UCC November5   Nov UCCLO 1062  0.9 
1.2 N   17  0.29488545  1.429058721 11.89594224 1.51
-31.96  1.6152.94   yes
11  UCC November5   Nov UCCLO 1163  1.3 
2   N   14  0.241601092 3.29815495  4.244797535 
no
12  UCC November5   Nov UCCLO 1264  1.2 
1.3 N   11  0.261040739 1.610353496 6.83079835  2.62
-28.94  1.4651.9yes
13  UCC November5   Nov UCCLO 1365  1.2 
1.3 N   13  0.238863129 2.221057396 5.853068012 1.13
-28.81  2.0851.43   yes
14  UCC November5   Nov UCCLO 1466  1.1 
1.5 N   9   0.309603194 2.859756011 3.14712163  
no
15  UCC November5   Nov UCCLO 1567  1.1 
1.3 N   18  0.383441504 2.949059627 6.103640576 1.51
-30.14  1.6552.04   yes
16  UCC November5   Nov UCCLO 1668  1.3 
2.7 N   13  0.269711187 1.430856375 9.085468137 1.99
-29.09  1.8751.21   yes
17  UCC November5   Nov UCCLO 1769  0.8 
1.4 N   13  0.245685997 3.808576972 3.41334837  
no
18  UCC November5   Nov UCCLO 1870  1.6 
1.8 N   11  0.271419599 2.305398713 4.771408926 2.94
-29.22  1.9351.46   yes
19  UCC November5   Nov UCCLO 1971  1   
1.5 N   18  0.338103566 2.303586185 7.813903435 2.93
-30.27  1.9251.51   yes
20  UCC November5   Nov UCCLO 2073  1.1 
1.2 N   11  0.27096196  3.230604699 3.404935307 
no
21  UCC November5   Nov UCCLO 2174  1.2 
1.5 N   10  0.294348983 3.319661403 3.012355414 
no
22  UCC November5   Nov UCCLO 2275  1.5 
1.9 N   12  0.230438536 2.935053987 4.088510825 1.74
-29.49  1.6450.28   yes
23  UCC November5   Nov UCCLO 2376  1.1 
1.4 N   14  0.264963659 3.689609021 3.794439985   

Re: [R] ggplot2

[James Henson]

Thanks, the stat="identity" worked.

On Tue, Apr 12, 2016 at 3:34 PM, Huzefa Khalil <huzefa.kha...@umich.edu>
wrote:

> Hi James,
>
> If you want to specify the y-values, you need to use stat="identity" as
> below:
>
> ggplot(probability, aes(x=Fertilizer, y=prob)) +
> geom_bar(stat="identity", aes(fill=Treatment))
>
>
> best,
> huzefa
>
> On Tue, Apr 12, 2016 at 1:02 PM, James Henson <jfhens...@gmail.com> wrote:
> > Dear R Community,
> >
> > Below is a problem with a simple ggplot2 graph. The code returns the
> error
> > message below.
> >
> > Error: stat_count() must not be used with a y aesthetic.
> >
> > My code is below and the data is attached as a ‘text’ file.
> >
> >
> >
> > # Graph of the probabilities
> >
> > library(digest)
> >
> > library(DT)
> >
> > datatable(probability)
> >
> > str(probability)
> >
> > probability$Fertilizer <- as.factor(probability$Fertilizer)
> >
> > str(probability)
> >
> > library(ggplot2)
> >
> > plot1 <- ggplot(probability, aes(x=Fertilizer, y=prob)) +
> > geom_bar(aes(fill=Treatment))
> >
> > plot1
> >
> >
> >
> > Thanks.
> >
> > Best regards,
> >
> > James F. Henson
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] ggplot2

[James Henson]

Dear R Community,

Below is a problem with a simple ggplot2 graph. The code returns the error
message below.

Error: stat_count() must not be used with a y aesthetic.

My code is below and the data is attached as a ‘text’ file.



# Graph of the probabilities

library(digest)

library(DT)

datatable(probability)

str(probability)

probability$Fertilizer <- as.factor(probability$Fertilizer)

str(probability)

library(ggplot2)

plot1 <- ggplot(probability, aes(x=Fertilizer, y=prob)) +
geom_bar(aes(fill=Treatment))

plot1



Thanks.

Best regards,

James F. Henson
Trt probLL  UL  Fertilizer  Treatment
S0  0.  0.0154  0.4998  0   S
S2  0.  0.0154  0.4998  2   S
S4  0.  0.0154  0.4998  4   S
S6  0.  0.0154  0.4998  6   S
P0  0.  0.056   0.579   0   P
P2  0.7778  0.4208  0.9439  2   P
P3  0.333   0.  0.6665  4   P
P4  0.6667  0.3334  0.  6   P
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] installing packages

[James Henson]

To All,
Thanks for your help.

I uninstalled R, the 3.2 library and R Studio.  Reinstalled R and R Studio.
Now the temp files move the newly installed packages into the
R-.23.2.4revised library.

> .libPaths()
[1] "C:/Users/james_henson/Desktop/Documents/R/win-library/3.2"
[2] "C:/Program Files/R/R-3.2.4revised/library"





On Mon, Mar 21, 2016 at 9:57 PM, Jeff Newmiller <jdnew...@dcn.davis.ca.us>
wrote:

> I hope not. That directory is not for working in. suggestion to restart R
> sounds most likely to fix the issue.
> --
> Sent from my phone. Please excuse my brevity.
>
> On March 21, 2016 2:10:01 PM PDT, KMNanus <kmna...@gmail.com> wrote:
>>
>> Have you set your working directory to the “3.2” folder?
>> Ken
>> kmna...@gmail.com
>> 914-450-0816 (tel)
>> 347-730-4813 (fax)
>>
>>
>>
>>  On Mar 21, 2016, at 5:07 PM, James Henson <jfhens...@gmail.com> wrote:
>>>
>>>  Dear R community,
>>>
>>>  When I install or update a package, R prints the waring below.  I go to the
>>>  ‘downloaded_packages’ folder in the Temp file and manually move the new or
>>>  updated package to the folder ‘3.2’.   How can I instruct R to download new
>>>  and updates packages into the ‘3.2’ folder?
>>>
>>>  Warning in install.packages :
>>>
>>>   unable to move temporary installation
>>>  
>>> ‘C:\Users\james_henson\Desktop\Documents\R\win-library\3.2\file1c5c6f1731c8\nlme’
>>>  to ‘C:\Users\james_henson\Desktop\Documents\R\win-library\3.2\nlme
>>>
>>>
>>>
>>>  The downloaded binary packages are in
>>>
>>>
>>>  C:\Users\james_henson\AppData\Local\Temp\RtmpIZmUa3\downloaded_packages
>>>
>>>
>>>
>>>  Thank for your help.
>>>
>>>  James F. Henson
>>>
>>>   [[alternative HTML version deleted]]
>>>
>>> --
>>>
>>>  R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>>  https://stat.ethz.ch/mailman/listinfo/r-help
>>>  PLEASE do read the posting guide 
>>> http://www.R-project.org/posting-guide.html
>>>  and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>> --
>>
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] installing packages

[James Henson]

Dear R community,

When I install or update a package, R prints the waring below.  I go to the
‘downloaded_packages’ folder in the Temp file and manually move the new or
updated package to the folder ‘3.2’.   How can I instruct R to download new
and updates packages into the ‘3.2’ folder?

Warning in install.packages :

  unable to move temporary installation
‘C:\Users\james_henson\Desktop\Documents\R\win-library\3.2\file1c5c6f1731c8\nlme’
to ‘C:\Users\james_henson\Desktop\Documents\R\win-library\3.2\nlme



The downloaded binary packages are in


C:\Users\james_henson\AppData\Local\Temp\RtmpIZmUa3\downloaded_packages



Thank for your help.

James F. Henson

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] package broom

[James Henson]

Dear R community

My version is R version 3.2.3.
The package "broom" appears to install, but it will not load.
The error message is below.


> library(broom)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck
= vI[[j]]) :
  there is no package called ‘mnormt’
Error: package or namespace load failed for ‘broom’


Thanks,
James F. Henson

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] contrasts among simple effects

[James Henson]

Greetings R Community

My goal is to make orthogonal contrasts among simple effects in analysis of
repeated measures data.  The SAS publication, on page 1224, shows how to
make this type of contrasts in SAS.  But, my search of books about repeated
measures analysis using R, and on-line has not yielded a methodology.
Hopefully, someone can direct me to a book or publication that will show me
a methodology.

Statistical Analysis of Repeated Measures Data Using SAS Procedures

http://cslras.pbworks.com/f/littell_j_anim_sci_76_4_analysis_of_repeated_measures_using_sas.pdf



Attached is a csv data file (file name = heartRate.csv).  My code for the
repeated measures analysis is below.


library("nlme")

# with AR1 variance/covariance structure, with ordered statement

heartRate$time <- factor(heartRate$time)

model2a <- lme(HR ~ drug*ordered(time), random =~1|person, correlation
=corAR1(, form=~1|person), data = heartRate)

summary(model2a)

anova(model2a)


Making a new variable ‘simple’ that merges the variables drug and time will
enable me to make orthogonal contrasts among the simple effects.  But, when
using the variable ‘simple’ as the independent variable, the data will no
longer be fitted to the AR1 variance/co-variance structure.

Thanks.

Best regards,

James F.Henson
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] contrasts among simple effects - 2

[James Henson]

Greetings R Community

Apologize for previously sending a csv file.

My goal is to make orthogonal contrasts among simple effects in analysis of
repeated measures data.  The SAS publication, on page 1224, shows how to
make this type of contrasts in SAS.  But, my search of books about repeated
measures analysis using R, and on-line has not yielded a methodology.
Hopefully, someone can direct me to a book or publication that will show me
a methodology.

Statistical Analysis of Repeated Measures Data Using SAS Procedures

http://cslras.pbworks.com/f/littell_j_anim_sci_76_4_analysis_of_repeated_measures_using_sas.pdf



Attached is a txt data file (file name = heart_rate.txt).  My code for the
repeated measures analysis is below.

library("nlme")

# with AR1 variance/covariance structure, with ordered statement

heartRate$time <- factor(heartRate$time)

model2a <- lme(HR ~ drug*ordered(time), random =~1|person, correlation
=corAR1(, form=~1|person), data = heartRate)

summary(model2a)

anova(model2a)


Making a new variable ‘simple’ that merges the variables drug and time will
enable me to make orthogonal contrasts among the simple effects.  But, when
using the variable ‘simple’ as the independent variable, the data will no
longer be fitted to the AR1 variance/covariance structure.

Thanks.

Best regards,

James F.Henson
drugperson  timeHR
a   1   1   72
a   4   1   78
a   7   1   71
a   10  1   72
a   13  1   66
a   16  1   74
a   19  1   62
a   22  1   69
b   2   1   85
b   5   1   82
b   8   1   71
b   11  1   83
b   14  1   86
b   17  1   85
b   20  1   79
b   23  1   83
c   3   1   69
c   6   1   66
c   9   1   84
c   12  1   80
c   15  1   72
c   18  1   65
c   21  1   75
c   24  1   71
a   1   2   86
a   4   2   83
a   7   2   82
a   10  2   83
a   13  2   79
a   16  2   83
a   19  2   73
a   22  2   75
b   2   2   86
b   5   2   86
b   8   2   78
b   11  2   88
b   14  2   85
b   17  2   82
b   20  2   83
b   23  2   84
c   3   2   73
c   6   2   62
c   9   2   90
c   12  2   81
c   15  2   72
c   18  2   62
c   21  2   69
c   24  2   70
a   1   3   81
a   4   3   88
a   7   3   81
a   10  3   83
a   13  3   77
a   16  3   84
a   19  3   78
a   22  3   76
b   2   3   83
b   5   3   80
b   8   3   70
b   11  3   79
b   14  3   76
b   17  3   83
b   20  3   80
b   23  3   78
c   3   3   72
c   6   3   67
c   9   3   88
c   12  3   77
c   15  3   69
c   18  3   65
c   21  3   69
c   24  3   65
a   1   4   77
a   4   4   81
a   7   4   75
a   10  4   69
a   13  4   66
a   16  4   77
a   19  4   70
a   22  4   70
b   2   4   80
b   5   4   84
b   8   4   75
b   11  4   81
b   14  4   76
b   17  4   80
b   20  4   81
b   23  4   81
c   3   4   74
c   6   4   73
c   9   4   87
c   12  4   72
c   15  4   70
c   18  4   61
c   21  4   68
c   24  4   63
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] [FORGED] Re: Dunnett Test in 'multicomp' package

[James Henson]

Thanks. A useful tip for a long-time SAS user.
James F. Henson

On Fri, Jun 5, 2015 at 3:47 AM, Gerrit Eichner 
gerrit.eich...@math.uni-giessen.de wrote:

 Hello, everyone,

 aside from Rolf's hint (and Richard's warning!) you could also consider
 relevel():

 viagraData$dose - relevel( viagraData$dose, ref = placebo)

  Hth  --  Gerrit


 On Fri, 5 Jun 2015, Rolf Turner wrote:

  On 05/06/15 11:08, Jim Lemon wrote:

 Hi James,
 You can change the order of levels like this:

 levels(viagraData$dose)-c(placebo,low dose,high dose)


 SNIP

 As Richard Heiberger has pointed out, this is wrong.

 What *does* work is:

 viagraData$dose)-factor(viagraData$dose,
levels=c(placebo,low dose,high dose)

 This is a trap into which many a Young Player (including my very good
 self) has fallen.

 cheers,

 Rolf Turner



 --
 Technical Editor ANZJS
 Department of Statistics
 University of Auckland
 Phone: +64-9-373-7599 ext. 88276

 __
 R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.


 __
 R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.


[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.